initialise repository

_quarto.yml

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+project:
+  type: website
+
+website:
+  title: "BM432 Project Pages"
+  site-url: https://sipbs-compbiol.github.io/bm432-project
+  navbar:
+    logo: ./assets/images/sipbs_compbio.png
+    right:
+      - text: "Home"
+        file: index.qmd
+      - text: "Project Guidance"
+        menu: 
+          - text: "Key Dates"
+            href: calendar.qmd
+          - text: "Project Expectations"
+            href: expectations.qmd
+          - text: "Project and Time Management"
+            href: time_management.qmd
+      - text: "Computational Biology"
+        menu:
+          - text: "Learning Resources"
+            href: learning_resources.qmd
+          - text: "Online Resources"
+            href: online_resources.qmd
+          - text: "Software Tools"
+            href: software.qmd
+      - text: "Thesis and Presentation"
+        menu: 
+          - text: "Thesis"
+            href: thesis.qmd
+          - text: "Presentation"
+            href: presentation.qmd
+          - text: "Science Communication"
+            href: scicomm.qmd
+      - icon: github
+        href: https://github.com/sipbs-compbiol/sipbs-internships
+      - icon: twitter
+        href: https://twitter.com/scompbiol
+      - icon: rss
+        href: index.xml  
+  page-footer: 
+    left: This site © University of Strathclyde 2023
+
+
+format:
+  html:
+    theme: simplex
+    toc: true
+    css: styles.css
+    embed-resources: true
+
+editor: source
+
+execute:
+  freeze: auto

_variables.yml

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+admin:
+  name: "Leighton Pritchard"
+  email: "[email protected]"
+  homepage: "https://www.strath.ac.uk/staff/pritchardleightondr/"
+
+ay: "AY2023-24"
+
+myplace:
+  course: "BM432: Being a Biomolecular Scientist 4"
+  link: "https://classes.myplace.strath.ac.uk/course/view.php?id=21920"
+  timeline: "https://classes.myplace.strath.ac.uk/mod/resource/view.php?id=1873811"
+  runningorder: "https://classes.myplace.strath.ac.uk/mod/resource/view.php?id=1873812"

about.qmd

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+---
+title: "About"
+---
+
+About this site
+
+```{r}
+1 + 1
+```

bm432-project.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

calendar.qmd

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+---
+title: "Key Dates"
+description: |
+ Key Dates for {{< var ay >}} BM432 Final Year Projects
+tbl-colwidths: [5, 10, 50, 5]
+number-sections: true
+about:
+  template: marquee
+  links:
+    - icon: twitter
+      text: Twitter
+      href: https://twitter.com/scompbiol
+    - icon: github
+      text: Github
+      href: https://github.com/sipbs-compbiol
+    - icon: envelope
+      text: Email
+      href: mailto:[email protected]
+html:
+  anchor-sections: true      
+---
+
+- BM432 Project Timeline [(MyPlace {{< bi link >}})]({{< var myplace.timeline >}})
+- BM432 Running Order (Workshops) [(MyPlace {{< bi link >}})]({{< var myplace.runningorder >}})
+
+## Calendar
+
+This is an **indicative** calendar for SIPBS CompBiol Group BM432 projects in {{< var ay >}}.
+
+::: {.callout-warning}
+**This calendar is indicative only**. Please consult with the official course [MyPlace]({{< var myplace.link >}}) page for submission dates, deadlines, and other timings. Links to useful documents are provided above.
+:::
+
+### Semester 1
+
+| Week  | Date/Time    | Activity                               | Responsibility |
+| ----- | :----------- | :------------------------------------- | :------------: |
+| **1** | w/b Mon 18/9 | **Suggested activities** <br> - read papers in project description <br> - literature search <br> | |
+| **1** | **Thu 21/9** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** <br> - Introductions <br> - Project descriptions <br> - Project expectations <br> - Learning agreement <br> - Project management resources | **LP**
+| **1** | **Fri 22/9** | **Submit Learning Agreement** <br> ([MyPlace]({{< var myplace.link >}})) | **Students** |
+| **2** | w/b Mon 25/9 | **Suggested activities** <br> - Continue literature search <br> - Practice project management tools | |
+| **2** | **Thu 28/9** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** <br> - Discuss task for next week (choose one paper each for mini journal club) <br> - Computational and bioinformatics tools | **LP** |
+| **3** | w/b Mon 2/10 | **Suggested activities** <br> - Continue literature search <br> - Practice computational and bioinformatics tools | |
+| **3** | **Fri 6/10** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** <br> - Mini journal club. Each student leads a short (15min) discussion of their chosen paper. | **LP** |
+| **3** | **Fri 6/10** | **Complete Workshop 4 - Safety tasks** | **Students** |
+| **4** | w/b Mon 9/10 | **Suggested activities** <br> Continue literature search Outline thesis introduction | |
+| **4** | **Fri 13/10** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** How to write a project thesis | **LP** |
+| **4** | **Fri 13/10** | **Complete Workshop 5 quizzes - Ethics** <br> ([MyPlace]({{< var myplace.link >}})) | **Students** |
+| **5** | w/b Mon 16/10 | **Suggested activities** <br> Continue literature search Writing thesis introduction | |
+| **5** | **Mon 16/10** | **Submit draft Introduction/Literature Review** <br> ([MyPlace]({{< var myplace.link >}})) | **Students** |
+| **5** | **Fri 20/10** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** Feedback/discussion of thesis outlines Project planning discussion | **LP** |
+| **6** | w/b Mon 23/10 | **Suggested activities** <br> Project work | |
+| **6** | **Fri 27/10** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** Project planning discussion | **LP** |
+| **7** | w/b Mon 30/10 | **Suggested activities** <br> Project work | |
+| **7** | **Fri 3/11** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** Project updates and discussion | **LP** |
+| **8** | w/b Mon 6/11 | **Suggested activities** <br> Project work | |
+| **8** | **Fri 10/11** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** Project updates and discussion | **LP** |
+| **9** | w/b Mon 13/11 | **Suggested activities** <br> Project work | |
+| **9** | **Fri 17/11** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** Project updates and discussion | **LP** |
+| **10** | w/b Mon 20/11 | **Suggested activities** <br> Project work | |
+| **10** | **Fri 24/11** <br> 14:00-15:00 <br> HW324 | **Project Group Meeting** Project updates and discussion | **LP** |
+| **11** | w/b Mon 27/11 | **Suggested activities** <br> Project work | |
+| **11** | **Mon 27/11** | **Submit presentation PowerPoint File** <br> ([MyPlace]({{< var myplace.link >}})) | **Students** |
+| **11** | **Thu 30/11** | **Project Presentations** | **Students** |
+| **11** | **Fri 31/11** <br> 14:00-15:00 <br> HW324 | **FINAL Project Group Meeting** Project updates and discussion | **LP** |
+
+### Semester 2
+
+| Week  | Date/Time    | Activity                               | Responsibility |
+| ----- | :----------- | :------------------------------------- | :------------: |
+| **3** | **Mon 29/1** | **Submit draft thesis**  <br> ([MyPlace]({{< var myplace.link >}})) | **Students** |
+| **3** | **Mon 26/2** | **Submit final thesis**  <br> ([MyPlace]({{< var myplace.link >}})) | **Students** |

index.qmd

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+---
+title: "SIPBS CompBiol BM432 Project Pages"
+image: ./assets/images/sipbs_compbio.png
+about:
+  template: trestles
+  links:
+    - icon: twitter
+      text: Twitter
+      href: https://twitter.com/scompbiol
+    - icon: github
+      text: Github
+      href: https://github.com/sipbs-compbiol
+    - icon: envelope
+      text: Email
+      href: mailto:[email protected]
+---
+
+Welcome to the SIPBS CompBiol Group BM432 project pages!
+
+## What is this site for?
+
+This site is designed to assist you as you complete your final year honours project and thesis in the SIPBS CompBiol group. These pages should be read in conjunction with the official SIPBS Internship Materials available on the course [MyPlace page]({{< var myplace.link >}})
+
+We have grouped information under three main headings: 
+
+- Project Guidance, which includes key dates, and tips on project and time management
+- Computational Biology, providing links to online learning, databases, software, and other resources that may be helpful to you
+- Thesis and Presentation, with links and advice on how to structure and present your work for others
+
+## Getting Started
+
+### Project Work
+
+Please do read the [Project Expectations](expectations.qmd) page, and keep the [Key Dates](calendar.qmd) in mind as you carry out your project, as these outline what you should be doing, and when, to keep on track with the project. Especially if this is your first time working on a long-form scientific project, or producing a dissertation of this length, please also take time to read our advice on [Project and Time Management](time_management.qmd), and how to go about [writing a thesis](thesis.qmd).
+
+We also provide advice on [giving scientific presentations](presentation.qmd) - an important component of your project - and [Science Communication](scicomm.qmd) in general. While tailored towards the BM432 project, the advice is quite general and we hope it will be helpful for some time to come.
+
+### Computational Biology and Bioinformatics
+
+If you are new to computational biology and bioinformatics, projects in this area can be quite challenging. While we design our projects to be as accessible as possible to students with no background in the field, it is unavoidable that you will need to learn new concepts, skills, and tools. We have compiled sets of [Learning Resources](learning_resources.qmd) that can help you with the self-directed learning you may need.
+
+As you may be unfamiliar with the wide scope of bioinformatics and computational biology tools and resources available, we have also compiled sets of [Online Resources](online_resources.qmd) - databases, online services, and other important sites - that may be directly useful for your project. We have also compiled sets of [Software Tools](software.qmd) that you may be able to download and use on your own computer.
+
+## Acknowledgements
+
+These pages were originally developed in 2023 by Dr {{< var admin.name >}} and Dr Morgan Feeney, and are currently maintained by, [Dr {{< var admin.name >}}](%7B%7B%3C%20var%20admin.homepage%20%3E%7D%7D).
+
+These materials are © University of Strathclyde, and licensed under the [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](https://creativecommons.org/licenses/by-nc-sa/4.0/). Linked and embedded materials are governed by their own licenses. I assume that all external materials used or embedded here are covered under the educational fair use policy. If this is not the case and any material displayed here violates copyright, please let [me](%7B%7B%3C%20var%20admin.email%20%3E%7D%7D) know and I will remove it.

styles.css

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+/* css styles */